Festo Massawe

The potential for underutilized crops to improve security of food production

Staple crops face major challenges in the near future and a diversification away from over-reliance on staples will be important as part of the progress towards the goal of achieving security of food production. Underutilized or neglected crops species are often indigenous ancient crop species which are still used at some level within the local, national or even international communities, but have the potential to contribute further to the mix of food sources than they currently do. The most cost-effective and easily disseminated changes that can be made to a crop are changes to the genetics, as these are contained within the seed itself and, for many species, the seed is a pure breeding, self-replicating, resource. This article focuses on the potential of underutilized crops to contribute to food security and, in particular, whether genetics and breeding can overcome some of the constraints to the enhanced uptake of these species in the future. The focus here is on overview rather than detail and subsequent articles will examine the current evidence base.

ASSESSING THE POTENTIAL OF AN UNDERUTILIZED CROP – A CASE STUDY USING BAMBARA GROUNDNUT

Using experience with bambara groundnut ( Vigna subterranea ), this paper examines how local knowledge, genetic evaluation, research in fields, glasshouses and laboratories, and crop simulation modelling might be linked within a methodological framework to assess rapidly the potential of any underutilized crop. The approach described is retrospective in that each activity was not clearly defined and structured at the outset. However, the experience gained may help to establish a methodology by which growers, researchers and international agencies can integrate their knowledge and understanding of any particular underutilized crop and apply similar principles to accelerate the acquisition of knowledge on other underutilized species. The use of a methodological framework provides a basis for activities that maximize knowledge, minimize duplication of effort, identify priority areas for further research and dissemination, and derive general principles for application across underutilized crops in general. It also allows policy makers and planners to make comparative decisions on the nutritional, economic and research importance of different underutilized and more-favoured species. In particular, the incorporation of a generic crop simulation model within the methodological framework may assist growers, extension agencies and scientists to refine general recommendations for any particular crop to local conditions. Also, the incorporation of information gathered from the field, laboratory or market can be used to update rapidly the predictive capacity of the model for each crop.

Crop Diversity: An Unexploited Treasure Trove for Food Security

The prediction is that food supply must double by 2050 to cope with the impact of climate change and population pressure on global food systems. The diversification of staple crops and the systems in which they grow is essential to make future agriculture sustainable, resilient, and suitable for local environments and soils.

Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces assessed by Random Amplified Polymorphic DNA (RAPD) markers

Genetic diversity in 12 landraces of bambara groundnut (Vigna subterranea), an indigenous African legume, was evaluated using Random Amplified Polymorphic DNA (RAPD) markers. DNA from individuals of each landrace was also analysed to determine the level of heterogeneity within landraces. RAPDs revealed high levels of polymorphism among landraces. The percentage polymorphism ranged from 63.2% to 88.2% with an average of 73.1% for the 16 RAPD primers evaluated. The construction of genetic relationships using cluster analysis groups the 12 landraces in two clusters. RAPDs are useful for the genetic diversity studies in V. subterranea and can identify variation within landraces.

Diversifying crops for food and nutrition security - a case of teff.

There are more than 50000 known edible plants in the world, yet two‐thirds of global plant‐derived food is provided by only three major cereals – maize (Zea mays), wheat (Triticum aestivum) and rice (Oryza sativa). The dominance of this triad, now considered truly global food commodities, has led to a decline in the number of crop species contributing to global food supplies. Our dependence on only a few crop species limits our capability to deal with challenges posed by the adverse effects of climate change and the consequences of dietary imbalance. Emerging evidence suggests that climate change will cause shifts in crop production and yield loss due to more unpredictable and hostile weather patterns. One solution to this problem is through the wider use of underutilised (also called orphan or minor) crops to diversify agricultural systems and food sources. In addition to being highly nutritious, underutilised crops are resilient in natural and agricultural conditions, making them a suitable surrogate to the major crops. One such crop is teff [Eragrostis tef (Zucc.) Trotter], a warm‐season annual cereal with the tiniest grain in the world. Native to Ethiopia and often the sustenance for local small farmers, teff thrives in both moisture‐stressed and waterlogged soil conditions, making it a dependable staple within and beyond its current centre of origin. Today, teff is deemed a healthy wheat alternative in the West and is sought‐after by health aficionados and those with coeliac disease or gluten sensitivity. The blooming market for healthy food is breathing new life into this underutilised crop, which has received relatively limited attention from mainstream research perhaps due to its ‘orphan crop’ status. This review presents the past, present and future of an ancient grain with a potential beyond its size.

SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces

We report here the development of 75 SSR markers for Bambara groundnut through various sequencing approaches and the subsequent utilization of these SSR markers and other marker types (DArT Arrays) for the analysis of genetic diversity, population structure and the selection of pure lines from landraces. To assess the level of genetic diversity in Bambara groundnut landrace collections, 68 and 201 polymorphic SSR and DArT markers, respectively, were assayed against 24 single individual seed from a core collection of landraces. Polymorphic information content (PIC) ranged from 0.08 to 0.89 with an average of 0.42 across all SSR polymorphic markers, with observed (Ho) and expected (He) heterozygosity of 0.01 and 0.5 respectively. For the population structure analysis, 12 SSR markers selected as highly polymorphic from the initial screen were assayed against 123 landrace accessions. The average PIC across the 12 SSR was 0.66 with an average Ho of 0.02 and an inbreeding coefficient (f) of 0.98, suggesting that seed derived from a single plant essentially represents an unselected variety. Based on the low level of Ho and high f observed in the landrace samples, a subset of 35 genotypes derived from the landraces were advanced for field trials in Botswana and scored for 37 phenotypic traits. These 35 individual genotypes were ranked for agronomic performance based on yield component factors and other qualitative traits after field evaluation. Five genotypes with good yield potential and adaptability were recommended as potential varieties for Botswanan agro-ecology.

Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis.

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an African legume and is a promising underutilized crop with good seed nutritional values. Low temperature stress in a number of African countries at night, such as Botswana, can effect the growth and development of bambara groundnut, leading to losses in potential crop yield. Therefore, in this study we developed a computational pipeline to identify and analyze the genes and gene modules associated with low temperature stress responses in bambara groundnut using the cross-species microarray technique (as bambara groundnut has no microarray chip) coupled with network-based analysis. Analyses of the bambara groundnut transcriptome using cross-species gene expression data resulted in the identification of 375 and 659 differentially expressed genes (p<0.01) under the sub-optimal (23°C) and very sub-optimal (18°C) temperatures, respectively, of which 110 genes are commonly shared between the two stress conditions. The construction of a Highest Reciprocal Rank-based gene co-expression network, followed by its partition using a Heuristic Cluster Chiseling Algorithm resulted in 6 and 7 gene modules in sub-optimal and very sub-optimal temperature stresses being identified, respectively. Modules of sub-optimal temperature stress are principally enriched with carbohydrate and lipid metabolic processes, while most of the modules of very sub-optimal temperature stress are significantly enriched with responses to stimuli and various metabolic processes. Several transcription factors (from MYB, NAC, WRKY, WHIRLY & GATA classes) that may regulate the downstream genes involved in response to stimulus in order for the plant to withstand very sub-optimal temperature stress were highlighted. The identified gene modules could be useful in breeding for low-temperature stress tolerant bambara groundnut varieties.

Development of gene‐based SSR markers in winged bean (Psophocarpus tetragonolobus (L.) DC.) for diversity assessment

Winged bean (Psophocarpus tetragonolobus) is an herbaceous multipurpose legume grown in hot and humid countries as a pulse, vegetable (leaves and pods), or root tuber crop depending on local consumption preferences. In addition to its different nutrient-rich edible parts which could contribute to food and nutritional security, it is an efficient nitrogen fixer as a component of sustainable agricultural systems. Generating genetic resources and improved lines would help to accelerate the breeding improvement of this crop, as the lack of improved cultivars adapted to specific environments has been one of the limitations preventing wider use. A transcriptomic de novo assembly was constructed from four tissues: leaf, root, pod, and reproductive tissues from Malaysian accessions, comprising of 198,554 contigs with a N50 of 1462 bp. Of these, 138,958 (70.0%) could be annotated. Among 9682 genic simple sequence repeat (SSR) motifs identified (excluding monomer repeats), trinucleotide-repeats were the most abundant (4855), followed by di-nucleotide (4500) repeats. A total of 18 SSR markers targeting di- and tri-nucleotide repeats have been validated as polymorphic markers based on an initial assessment of nine genotypes originated from five countries. A cluster analysis revealed provisional clusters among this limited, yet diverse selection of germplasm. The developed assembly and validated genic SSRs in this study provide a foundation for a better understanding of the plant breeding system for the genetic improvement of winged bean.

Genomic structure and characterization of a lipase class 3 gene and promoter from oil palm.

Lipase class 3 is part of the triacylglycerol lipase family involved in lipid degradation, esterification, and transesterification processes in plants. In this study, a lipase class 3 gene and promoter from oil palm (Elaeis guineensis Jacq.) were isolated and characterized by Northern blot, Southern blot, oil palm genome sequence, and transient expression GUS assay. The full-length lipase class 3 (FLL1) deduced polypeptide encoded 483 amino acids and was identical to that deduced from lipase (EgLip1) cDNA (GI: 409994625). It contained the lipase consensus sequence, GxSxG motif, and a putative catalytic triad and had a 3-dimensional protein model similar to that of a lipase from Giberella zeae with a 50 % identity. The Northern blot and reverse transcription polymerase chain reaction (RT-PCR) show that FLL1 was predominantly expressed in the mesocarp and the expression increased as fruits reached maturity. A lower expression was detected in germinated seedlings and especially in roots. The expression of FLL1 was also enhanced in the mesocarp of cold treated fruits. A high oil accumulation in the mesocarp during fruit development makes this tissue a suitable target for a genetic modification, hence the isolation of the FLL1 promoter. The transient expression of the β-glucuronidase (GUS) gene driven by the FLL1 promoter detected the GUS expression in mesocarp slices, especially in vascular bundles. This suggests the potential role of using the promoter as tool to direct the expression of a transgene to the mesocarp of transgenic oil palm.

Beyond landraces: developing improved germplasm resources for underutilized species – a case for Bambara groundnut

The potential for underutilized crops (also known as minor, neglected or orphan crops) to improve food and nutrition security has been gaining prominence within the research community in recent years. This is due to their significance for diversified agricultural systems which is a necessary component of future agriculture to address food and nutritional security concerns posed by changing climate and a growing world population. Developing workable value chain systems for underutilized crop species, coupled with comparative trait studies with major crops, potentially allows us to identify suitable agricultural modalities for such species. Bambara groundnut (Vigna subterranea L. Verdc.), an underutilized leguminous species, is of interest for its reported high levels of drought tolerance in particular, which contributes to environmental resilience in semi-arid environments. Here, we present a synopsis of suitable strategies for the genetic improvement of Bambara groundnut as a guide to other underutilized crop species. Underutilized crops have often been adapted over thousands of years in particular regions by farmers and largely still exist as landraces with little or no genetic knowledge of key phenotypic traits. Breeding in these species is fundamentally different to breeding in major crops, where significant pedigree structures and history allow highly directed improvement. In this regard, deploying new integrated germplasm development approaches for variety development and genetic analysis, such as multi-parent advance generation inter-crosses (MAGIC), within breeding programmes of underutilized species will be important to be able to fully utilize such crops.